kkonganti@11: process MASHTREE { kkonganti@11: tag "$meta.id" kkonganti@11: label 'process_medium' kkonganti@11: kkonganti@11: module (params.enable_module ? "${params.swmodulepath}${params.fs}mashtree${params.fs}1.4.3" : null) kkonganti@11: conda (params.enable_conda ? "bioconda::mashtree=1.4.3 conda-forge::perl conda-forge::coreutils" : null) kkonganti@11: container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? kkonganti@11: 'https://depot.galaxyproject.org/singularity/mashtree:1.4.3--pl5321h031d066_0' : kkonganti@11: 'quay.io/biocontainers/mashtree:1.4.3--pl5321h031d066_0' }" kkonganti@11: kkonganti@11: input: kkonganti@11: tuple val(meta), path(seqs) kkonganti@11: path reference kkonganti@11: kkonganti@11: output: kkonganti@11: tuple val(meta), path("*.dnd"), emit: tree kkonganti@11: tuple val(meta), path("*.tsv"), emit: matrix kkonganti@11: tuple val(meta), path("*.nwk"), emit: nwk, optional: true kkonganti@11: path "versions.yml" , emit: versions kkonganti@11: kkonganti@11: when: kkonganti@11: task.ext.when == null || task.ext.when kkonganti@11: kkonganti@11: script: kkonganti@11: def args = task.ext.args ?: '' kkonganti@11: def prefix = task.ext.prefix ?: "${meta.id}" kkonganti@11: def fofn = (args.toString().matches(/.*file\-of\-files/) ? 'true' : 'false') kkonganti@11: def fas = reference.collect().join('\\n') kkonganti@11: def ref_fasta = (fas ?: '') kkonganti@11: """ kkonganti@11: kkonganti@11: echo -e "$ref_fasta" | while read -r fa; do kkonganti@11: if ! grep -F "\${fa}" $seqs && [ "$fofn" = "true" ]; then kkonganti@11: echo "\${fa}" >> $seqs kkonganti@11: fi kkonganti@11: done kkonganti@11: kkonganti@11: mashtree \\ kkonganti@11: $args \\ kkonganti@11: --tempdir "." \\ kkonganti@11: --numcpus $task.cpus \\ kkonganti@11: --outmatrix ${prefix}.tsv \\ kkonganti@11: --outtree ${prefix}.dnd \\ kkonganti@11: $seqs kkonganti@11: kkonganti@11: sed -ie 's/_scaffolded_genomic//g' ${prefix}.dnd kkonganti@11: cp ${prefix}.dnd ${prefix}.nwk kkonganti@11: kkonganti@11: cat <<-END_VERSIONS > versions.yml kkonganti@11: "${task.process}": kkonganti@11: mashtree: \$( echo \$( mashtree --version 2>&1 ) | sed 's/^.*Mashtree //' ) kkonganti@11: END_VERSIONS kkonganti@11: kkonganti@11: sedver="" kkonganti@11: grepver="" kkonganti@11: kkonganti@11: if [ "${workflow.containerEngine}" != "null" ]; then kkonganti@11: sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) kkonganti@11: grepver="\$sedver" kkonganti@11: else kkonganti@11: sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' ) kkonganti@11: grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' ) kkonganti@11: fi kkonganti@11: kkonganti@11: cat <<-END_VERSIONS >> versions.yml kkonganti@11: grep: \$grepver kkonganti@11: sed: \$sedver kkonganti@11: END_VERSIONS kkonganti@11: """ kkonganti@11: }